Calcium (Ca) and phosphorus (P) are critical nutrients and essential elements for the growth and development of humans. Since proper diagnosis and treatment are indispensable parts of personalized and precision medicine in patients with chronic diseases, in addition to unknown about the role of Ca/P ratios, the main aim of this cross-sectional study was to assess serum and urine Ca and P levels, the Ca/P ratios and their association with health and nutritional biomarkers in children and adolescents with chronic diseases. We carried out anthropometric, body composition, clinical evaluation, biochemical analysis, dietary survey, and bone densitometry methods. In 39 patients (2-19 years, 61.5% women, 56.4% adolescents), results showed that 20% of subjects had hypercalciuria, 23% had high Ca/Cr rate, and 44% exhibited hyperphosphaturia. No one patient was hypocalcemic or hyperphosphatemic. Serum and urinary Ca/P ratios were 2.12 and 0.13, respectively. 36% and 5% of subjects had hypophosphatemia and hypercalcemia, respectively. Serum and urine Ca and P levels were associated with several nutritional parameters studied. This study confirms the need to investigate Ca, P, and their relationship in urine in childhood.