A survey was conducted to assess livestock production systems and their constraints in smallholder dairy farmers in Lowlands and Highlands regions of Rwanda. A semi-structured questionnaire was administered to 247 and 145 households randomly selected in lowland (Rwamagana District) and highland (Musanze District), respectively. A Chi-square test was used to examine associations between categorical variables. Independent sample t-test was used to separate means. Excel Pivot table was used to rank raised constraints. Results showed that agro-ecological location had a significant influence (p<5%) on household characteristics; for gender of respondents (p=.019), gender of household head (p=0.012), age group of respondent (p=0.006), marital status of household head (p=.000), family members who live permanently in the household (p=0.025), education level of household head (p=0.003), primary activity of household head (p=.000) and source of dairy cattle (p=.000). It had a high significant influence (p<1%) on livestock production system; for feeding system (p=0.000); milking patterns (p=0.000); number of cattle per household (p=0.001); land allocation (p=0.005) and area for fodder production (p=.000). It had significant influences (p<5%) on the reproductive system; for the age at first artificial insemination (p=.000); number of calves born during the past 12 months (p=0.039) and average lactation length (p=0.043). It had a significant influence (p<5%) on sources of income; from cattle (p=.000); milk (p=0.034) and in farm yard manure (p=0.002). Farmers claimed fodder shortage as main constraint followed by land scarcity. They were challenged by high cost of inputs for milk production compared to the price of milk at farm gate and insufficiency of AI providers.