The method proposed in this paper focuses on problems of motion detection and counting of very small moving objects in videos. Existing video processing methods need a defined form or a sufficient size of moving objects and do not provide accurate results in the case of very small moving objects. Many false detections can occur or many moving objects can be missed. To deal with these problems, reliability coefficients are introduced on each step of the proposed detection method: A combination of these coefficients is used to rectify the counting result and characterize its precision. The proposed algorithm is applied to count migrating birds in videos made from observation points. Experiments show that the reliability coefficients significantly improve the counting process.