Bone and dental lesions have been documented in various deer species globally, affecting the efficiency of ingestion and digestion, consequently influencing their general health and leading to a decline in survival and reproductive performance. The present study aimed to characterize bone and dental lesions in the dry skulls of individual deer, estimate the prevalence of these lesions, and assess potential risk factors associated with the development of bone and dental alterations. This study assessed bone and dental lesions in 180 dry skulls of eleven neotropical deer species, originating from both captivity and wildlife conditions, through direct visual inspection. A high prevalence of bone and dental lesions was observed in all analyzed species. Dental calculus was the most common alteration (96.7%), followed by dental wear (71.1%). Animal age positively correlated with most bone and dental alterations, indicating that older animals showed more lesions. Additionally, the prevalence of these alterations was similar between sexes. Moreover, all lesions were more common in captive-bred animals, likely attributed to their older age and a less diverse diet. Blastocerus dichotomus and Mazama americana were most affected by bone resorption and dental trauma and had the highest dental calculus prevalence, along with Subulo gouazoubira and Passalites nemorivagus. All eleven species evaluated in the present study were susceptible to the occurrence of bone and dental lesions. Therefore, monitoring oral health and diet in captivity are fundamental practices for the conservation of these species.