Background: Malaria has been public health problem in Indonesia for a long period.  In Indonesia, population movement (migration) has a role in the spread of malaria especially in cross-border areas.

Purpose: The purpose of this study was to investigate risk factors of malaria infection status in cross-border area.

Methods: A case–control study was conducted to identify malaria risk factors associated with malaria in cross-border Purworejo district and Kulonprogo district. Cases (n = 138) were residents from the study area diagnosed with clinical malaria and recorded in Public Health Center. Controls (n = 138) were no identified malaria infection. Participants were interviewed face-to-face using a standard questionnaire to identify malaria risk factors in cross-border.  Analysis using univariate, bivariate with chi square test and calculate OR and multivariate with logistic regression. Logistic regression was used to calculate odds ratios (ORs) and 95% CI for risk factors after adjusting for socio-demographic characteristics.

Results: The results of the analysis showed that the most influential risk factors for the incidence malaria of cross-border were the location of the house > 500 meters dpl (OR=3.6; 95% CI 1.6-8.2), the walls of the house made of wood/bamboo (OR=2, 2; 95% CI 1.3-3.7), house spraying (0R=2.0; 95% CI 1.1-4.0), house distance 100 meters from mosquito breeding (OR=1.9 ; 95% CI 1.0-3.6).

Conclusion:The risk factors obtained can be taken into consideration in controlling malaria in cross-borders.