Animal facilities are increasing in size, while the availability of skilled workers is decreasing, thus, making it difficult for the farm laborers to ensure the health and well-being of all animals under their care. Passive Radio Frequency Identification (RFID) systems have been successfully used in animal facilities and research has identified potential applications in behavior monitoring for automated illness detection. While RFID signals range in frequency from 9 kHz to 5.8 GHz, the three most common frequencies are Low Frequency (LF, 125 kHz or 134.2 kHz), High Frequency (HF, 13.56 MHz), and Ultra-High Frequency (UHF, 865-868 MHz or 902-928 MHz). The objective of this article is to compare and evaluate the application of these three different RFID systems within large research facilities for livestock and poultry in terms of hardware characteristics, system design, and data processing and usage. Differences in tag construction, availability and cost are evident, but also basic differences in reader and antenna function, such as physics of communication, speed of detection, and anti-collision procedures exist. The systems have significant differences in reading ranges and are known to have varying influence of materials, especially water and metal, on the performance of the systems. However, the data streams, as well as methods of data processing and the creation of events (e.g., visits to a feeder), are similar for all systems. The characteristics mentioned do not necessarily identify an ideal RFID technology but reveal positive and negative aspects of each system. The three different RFID systems have been successfully applied in livestock and poultry facilities. Current research is focused on the utilization of the RFID data in prediction and decision models for illness, animal welfare, and management actions.