Parasite drug resistance is partly conferred by single nucleotide polymorphisms (SNPs) and monitoring these has been proposed as alternative to monitor drug resistance. Therefore, techniques are required facilitating analyses of multiple SNPs on epidemiological scale. We report a rapid and affordable microarray technique for application in epidemiological studies on malaria drug resistance. We have designed a multi-well microarray which is used in conjunction with PCR amplifid target genes implicated in drug resistance of malaria with subsequent one tube mini-sequencing using two fluorochromes. The drug resistance associated genes for pfdhfr, pfdhps, pfcrt, pfmdr1, and pfATPase were amplified and analysed in cultured P. falciparum strains and from field samples. We obtained a specificity of 94% compared to sequence data and comparison of field samples with RFLP typing resulted in an overall consistency of >90%, except for pfdhfr51 where most discrepancies were due to false determination in mixed infections by RFLP. The system is sufficiently sensitive to assay parasites in clinical malaria and in most asymptomatic cases and allows thus high throughput with minimal hands-on time. Cost for the assay have been calculated as 0.27 EURO/SNP (0.33 US$) which is below the cost incurred by other systems. Due to the simplicity of the approach newly identified SNPs can be incorporated rapidly. Such monitoring system makes it also possible to identify re-emergence of drug susceptible parasites once a drug has been withdrawn.