The objectives of this study were isolation and identification of bovine viral diarrhea virus (BVDV) from follicular fluid of buffalo ovaries by indirect immunofluoresence antibody technique (IFA) and reverse transcription-polymerase chain reaction (RT-PCR), histopathological findings as well as the effects of the virus on in vitro fertilization dynamics and embryos production system. Ovaries from 80 adult buffaloes were collected for BVDV isolation and identification, in vitro embryos production and histopathological study. Indirect immunofluoresence antibody technique revealed that 19 out of 60 animal (31.66%) were positive. A PCR on inoculated follicular fluid gave a highly specific sharp bands at the expected molecular weight 288 bp in 21 animal (19 IFA positive and other 2 IFA negative samples)/60 (35%). Bovine viral diarrhea virus infection caused a significance decrease (P<0.05) in the penetration and fertilization rates compared to the control (BVDV negative) group (35.62 and 20.55% versus 62.50 and 39.29%, respectively). Additionally, BVDV infection drastically reduced the cleavage rate, morula and blastocyst stages development (13.46, 2.63 and 0.00%) as compared with the control (31.82, 18.18 and 11.36%, respectively). Microscopically, a significant reduction in the number of follicles (antral, graafian and luteinized) and corpora lutea (albican, hemorrhagicum and luteum) was noticed in ovaries of animals positive for BVDV as compared with the control. Also, chronic oophoritis was observed in 17 out of 21 animal positive for BVDV along with edema and congested blood vessels. Mild edema and congested blood vessels were noticed in the interstitial tissue of cortical stroma in the other 4 animals. In conclusion, this work debated that BVDV infection has great potential effects on ovarian dynamics, structures, in vitro fertilization and buffalo embryo development.