Several studies suggest that reproductive performance in small-scale dairy farms is low reducing the farms’ profitability. Therefore, identifying risk factors associated with low reproductive performance is a key step to implement an improved reproductive management program. Accordingly, the aim of the present study was to identify the main risk factors affecting the reproductive performance of cows in small-scale dairy farms. Ninety-six dairy farms were incorporated into this study, and data from 1263 lactations were collected with different events as potential risk factors. Logistic regression models were used to assess the association (odds ratio, OR) and impact (population attributable fraction, PAF) between the potential risk factors and the reproductive variables. The main risk factors associated with assisted calving were male calf and primiparous cows (OR?=?1.7, PAF?=?0.315 and OR?=?1.5, PAF?=?0.131, respectively), while for retained fetal membranes (RFM) were assisted calving and abortion (OR?=?4.5, PAF?=?0.440 and OR?=?8.1, PAF?=?0.239, respectively). The main risk factors for days to first service over 70 days in milk were low body condition score at calving (BCS?≤?2.5) and primiparous cows (OR?=?2.2, PAF?=?0.285 and OR?=?1.4; PAF?=?0.096, respectively), while for days open over 110 days in milk were low BCS at calving (BCS?≤?2.5) and primiparous cows (OR?=?1.7, PAF?=?0.213 and OR?=?1.4; PAF?=?0.096, respectively) The main risk factor for non-pregnant cows at first service was RFM (OR?=?1.7; PAF?=?0.059). In conclusion, assisted calving, male calf, BCS?≤?2.5 and RFM were the main risk factors associated with reduced reproductive performance in small-scale dairy farms in tropical and subtropical regions of Mexico.