BACKGROUND: Peru has presented a decreasing malaria trend during the last decade, particularly in areas on northwestern coast; however, a limited number of cases continues to be reported yearly mainly in malaria hotspots. METHODS: A two-phase study was conducted to identify spatial and temporal clusters of incident Plasmodium vivax malaria, as well as to determine risk factors associated with households (HH) presenting P. vivax malaria episodes in an urban area of the northwestern Peruvian Coast from June 2008 to May 2010. In the first stage, a full census of the study population was conducted, including geo-referencing of reported P. vivax episodes. In the second stage, a population-based case-control study allowed the identification of risk factors associated with HHs reporting episodes. A total of 117 case HHs with reported P. vivax and 117 control HHs without malaria episodes were assessed. A semi-structured questionnaire was used to interview the head of households and to collect data on HH location and structure, availability of public services, preventive malaria measures, family member with outdoor occupation (farmer, moto-taxi driver), and other HH characteristics. Univariate and multivariate logistic regression analyses were performed to determine case-HH risk factors. SaTScan was used to detect spatial and temporal P. vivax malaria clusters. RESULTS: The most likely spatial cluster of malaria incidence included 1,040 people (22.4% of total population) in 245 HHs (24.6% of total HHs) accounting for 283 malaria episodes (40.1% of total episodes) during the study period (RR = 2.3, p < 0.001). A temporal cluster was also identified from April 12, 2009 to July 4, 2009 accounting for 355 malaria episodes (50.4% of total episodes) (RR = 7.2, p = 0.001). Factors significantly associated with case HHs compared with control HHs were: proximity to water drain < 200 metres (OR = 2.3, 95% CI: 1.3, 4.0); HH size >5 individuals (OR = 1.8, 95% CI: 1.0, 3.2); lack of potable water (OR = 1.8, 95% CI: 1.1, 3.2); and having domestic and peridomestic animals (OR = 3.6, 95% CI: 1.3, 9.5). CONCLUSION: Plasmodium vivax malaria incidence is highly heterogeneous in space and time in the urban study area with important geographical and housing risk factors associated with symptomatic episodes.