Bovine respiratory disease (BRD) is responsible for great economic losses in bovine production with major impact on family farming. Among all possible causes of bovine respiratory disease, viruses are commonly categorized as primary etiological agents. The present study aimed to identify the presence of bovine parainfluenza type 3 virus and Influenza virus D (IVD) in tracheobronchial fluid samples of healthy calves and calves showing clinical signs of bovine respiratory disease. Samples were collected from 42 family farming farms in São Paulo State, Brazil. A total of 141 tracheobronchial fluid samples from healthy calves (n=100) and calves showing clinical signs of bovine respiratory disease (n=41) were enrolled in this study. No sample was positive for both viruses after Real-Time PCR. Serum neutralization for bovine Parainfluenza type 3 virus (bPI-3v) was performed using 88 randomly selected serum samples and antibodies were detected in 45.45% (40/88) samples. Serum reactive samples were detected in both healthy (46.8%; 22/47) and BRD calves (43.9%; 18/41). Regarding antibody titer, numerical differences were detected between healthy (3%) and BRD calves (9%) for titers 128-512 (P > 0.05). The present research was the first that aimed to study the presence of bPI-3V and IVD in family farming herds from São Paulo State, Brazil. This research revealed that bPI-3v is circulating in the region studied and is possibly involved in some BRD cases. On the other hand, IVD was not detected.