During the 20 years of political violence in Peru starting in the late 1970’s, Ayacucho, an Andean department, was one of the most severely affected areas. Mass-migration to Lima increased largely driven by escaping from violence rather than by economic reasons. This provides a unique opportunity to study the effects of migration on health since selection biases are likely to be reduced. This study investigates differences in cardiovascular risk factors comparing three groups: i) always lived in Ayacucho (n=289); ii) migrated from Ayacucho to Lima (n=589); and, iii) always lived in Lima (n=199). A cross sectional design was used. A clear gradient of risk was seen for the majority of factors studied: body mass index (BMI), total and LDL-cholesterol, fasting blood glucose and insulin, CRP and fibrinogen, the rural group having the lowest risk, the urban group the highest. The migrant group had intermediate risk, although generally more similar to the urban than the rural group. Blood pressure did not show a clear gradient of difference between groups. The migrant group had similar systolic blood pressure (SBP) but lower diastolic blood pressure (DBP) than the rural group. The urban group had higher SBP but similar DBP than rural group. In the case of lipid profile, no difference was observed between groups for HDL and triglycerides. Obesity, diabetes, metabolic syndrome and estimated absolute cardiovascular risk were all higher in migrant and urban groups than in the rural sample. Within the migrant group, when classified by time since migration or age at migration, differences were observed in total cholesterol, LDL, fasting glucose and insulin resistance. The findings of this study suggest the impact of migration on cardiovascular risk is not uniform across risk factors. The study provides new insights into the increased disease risk associated with migration and urbanisation.