Soybean is one of the most important industrial crops in the world. The rich nutritional content of the seed is the reason for the increased cultivation of this crop all over the world. However, a large number of phytopathogenic fungi that exist in soybean seeds can reduce the nutritional content, germination, and seed vigor. Soybean seed samples were collected from experimental fields in seven locations in Vojvodina Province, Serbia in the period 2016-2018. From each sample, 100 seeds were randomly selected. Seeds were surface-disinfested in 4% sodium hypochlorite for 5 min, washed two times in sterile water, and dried on a filter paper. All 100 seeds were placed in 20 Petri dishes with standard potato dextrose agar medium (PDA), five seeds in each, and incubated at 22 ± 2°C for seven days, under 12 h of alternating light/dark conditions. The first assessment was performed on the fourth day after isolation. The health status analysis of soybean seed showed that Peronospora manshurica, Macrophominaphaseolina, Botrytis cinerea, Cercospora kikuchii as well as the species from genera Alternaria, Diaporthe, and Fusarium had colonized soybean seed in Serbia over three years. Species from the genus Alternaria and Peronospora manshurica were dominant in all three examined years. Furthermore, it has been noticed that weather conditions, location, and cultivar significantly influenced the intensity of the infection. The results of this study have shown which pathogens pose a threat to successful soybean seed production and help in finding preventive measures to control these pathogens during vegetation.