In this paper, we address the problem of car detection from aerial images using Convolutional Neural Networks (CNN). This problem presents additional challenges as compared to car (or any object) detection from ground images because features of vehicles from aerial images are more difficult to discern. To investigate this issue, we assess the performance of two state-of-the-art CNN algorithms, namely Faster R-CNN, which is the most popular region-based algorithm, and YOLOv3, which is known to be the fastest detection algorithm. We analyze two datasets with different characteristics to check the impact of various factors, such as UAV's altitude, camera resolution, and object size. The objective of this work is to conduct a robust comparison between these two cutting-edge algorithms. By using a variety of metrics, we show that YOLOv3 yields better performance in most configurations, except that it exhibits a lower recall and less confident detections when object sizes and scales in the testing dataset differ largely from those in the training dataset.