The determination of the vitamer 25(OH)D presents numerous analytical challenges due to its strong binding to the Vitamin D-Binding Protein (VDBP), the need to determine the equimolar amount of 25(OH)D
2 and 25(OH)D
3, the coexistence of numerous substances with similar chemical compositions that can cause cross-reactions, and the matrix effects such as interference from heterophilic antibodies or changes in protein composition [
9]. Analytical techniques for determining Vitamin D can be divided into two major groups: a) methods with complete removal of proteins and lipids before the analytical phase using organic solvents, including (liquid chromatography-mass spectrometry (LC-MS/MS), high performance liquid chromatography (HPLC), and radioimmunoassays (RIA); b) automated immunoassays that do not use organic solvents but alternative strategies to release the vitamin from the binding proteins [
9,
10,
11,
12]. The first method for determining 25(OH)D was published in 1971 and was a competitive method using rachitic rat serum as a source of the binding protein [
13]. In the late 1970s, several HPLC methods were developed, and in 1984, the first radioimmunoassay based on the use of a specific antibody [
14] was introduced. Subsequently, to overcome issues related to handling radioisotopes, enzyme immunoassays (EIA, ELISA) and chemiluminescent immunoassays (CLIA) were developed [
15]. These methods have become widely used in clinical laboratories due to progressive automation. However, these methods long suffered from poor standardization, preventing comparability of results obtained with different methods and from different laboratories. To address these issues, in 2010, the National Institutes of Health (NIH) initiated the Vitamin D Standardization Program (VDSP) in collaboration with the National Institute of Standards and Technology (NIST), the Centers for Disease Control and Prevention (CDC), Ghent University (Belgium), the American Association for Clinical Chemistry (AACC), the IFCC, and nutritional surveillance programs from various countries, including Australia, Canada, Germany, Ireland, Mexico, South Korea, the United Kingdom, and the USA [
16]. Thanks to this initiative, three reference measurement procedures (RMP) based on ID-LC-MS/MS and recognized by the Joint Committee for Traceability in Laboratory Medicine (JCTLM) are now available. Additionally, the National Institute of Standardization (NIST) developed a reference material (SRM) 972 and 972a, representing the second essential element for metrological traceability and standardization of measurement methods. Although the procedures of the reference methods are too complex and time-consuming for routine clinical practice, they provide reference (target) values that can be used to standardize or re-standardize methods used in clinical practice and make the results comparable. The issue of standardizing methods and the impact of this standardization on decision levels, which identify deficiency and desirable levels, is crucial given the significant discrepancies between the results of clinical studies conducted in recent years without methodological standardization. The lack of standardization has been shown to significantly alter the recommended levels for defining deficiency and insufficiency. For example, Binkley et al., commenting on two large clinical studies—the Third National Health and Nutrition Examination Survey (NHANES III, 1988-1994) and the German Health Interview and Examination Survey for Children and Adolescents (KIGGS, 2003-2006)—documented significant differences after reanalyzing the samples with a standardized method. After standardization, the percentage of vitamin D values below 30, 50, and 70 nmol/L in the KIGGS study increased from 28% to 47%, 13% to 87%, and 64% to 85%, respectively, while in the NHANES III study, the percentage of values below 30, 50, and 75 nmol/L increased from 4% to 6%, 22% to 31%, and 55% to 71%, respectively [
17]. Other authors have reported similar results [
18]. These significant differences lead to the conclusion that the levels recommended to date for identifying deficiency, insufficiency, and toxicity of vitamin D are compromised by the lack of method standardization. Consequently, new clinical trials with valid experimental designs and standardized methods need to be planned to accurately define the decision limits for deficiency, insufficiency, and possible toxicity of vitamin D. It also seems appropriate to revisit the literature data from recent years in light of these new findings, i.e., the variations related to methodological standardization. Regarding the methods to be used in the clinical laboratory, the choice between an automated immunoassay and an LC-MS/MS method depends on various factors such as the number of requests, the availability of qualified personnel in mass spectrometry techniques, and the specific instrumentation. Generally, data from external quality assessment programs demonstrate a continuous improvement in analytical performance: LC-MS/MS methods generally appear superior, with lower bias towards reference methods, but they exhibit greater variability reflecting existing differences in instrumentation, chromatographic separation, and calibration [
19]. Recent data show that only 20% of laboratories participating in EQA programs use LC-MS/MS methods, highlighting that automated immunoassays are still the most widely used [
10]. Very recently, Herrmann et al. proposed an innovative approach for diagnosing functional vitamin D deficiency based on the combined determination of 25(OH)D and its main catabolite (24, 25-dihydroxy-vitamin D) to calculate the so-called vitamin D metabolite ratio (VMR). According to the authors, the VMR allows for better identification of individuals with vitamin deficiency, as it is associated with significantly higher levels of PTH, accelerated bone metabolism, and mortality [
20]. These data, undoubtedly of interest, require further confirmation in clinical studies using appropriate experimental protocols. Conversely, the proposal to determine the free fraction of 25(OH)D, given that about 85-90% of the circulating fraction is bound to the specific protein (VDBP) and 10-15% to albumin, has been shown to have limited clinical utility for various reasons and could be reserved only for individuals with clinical conditions that significantly alter the concentration or affinity of the vitamin D-binding protein, such as cirrhosis, pregnancy, or acute inflammatory diseases [
21,
22,
23,
24].