Bovine viral diarrhea virus (BVDV) is a pestivirus of the Flaviviridae family that includes two biotypes, cytopathic (CP) and non-cytopathic (NCP). This study aimed to evaluate DNA damage and apoptosis in Madin-Darby Bovine Kidney (MDBK) cells following infection with both biotypes. MDBK monolayers were inoculated with a final dose of virus (10³ TCID₅₀ mL-1) and incubated for 24 h. DNA strand integrity was assessed using alkaline single-cell gel electrophoresis (SCGE), and DNA damage was quantified through Tail Moment (TM) and Olive Tail Moment (OTM) indices (n=3). Apoptosis was evaluated using Annexin V–FITC/PI flow cytometry to determine early and late apoptotic cell populations. Both biotypes significantly increased DNA fragmentation compared with the control group (p ≤ 0.05). TM values were 15.89 ± 2.13 (control), 57.63 ± 16.20 (NCP), and 68.15 ± 9.93 (CP), while OTM values were 8.71 ± 1.01 (control), 29.35 ± 9.18 (NCP), and 35.14 ± 6.90 (CP). Apoptosis analysis showed a higher percentage of apoptotic cells in infected groups, with CP BVDV inducing the greatest early and late apoptotic response, consistent with its cytopathic nature. Overall, both biotypes caused notable genomic injury and apoptosis in MDBK cells, with CP producing the highest level of damage, confirming SCGE combined with apoptosis assays as sensitive tools for detecting virus-mediated genomic instability and supporting their potential application in breeding programs aimed at enhancing resistance to infectious diseases.