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Abstract Background The main objective of this study was to assess the effectiveness of integrating the use of cell-phones into a routine malaria prevention and control programme, to improve the management of malaria cases among an under-served population in a border area. The module for disease and treatment monitoring of malaria (DTMM) consisted of case investigation and case follow-up for treatment compliance and patients' symptoms. Methods The module combining web-based and mobile technologies was developed as a proof of concept, in an attempt to replace the existing manual, paper-based activities that malaria staff used in treating and caring for malaria patients in the villages for which they were responsible. After a patient was detected and registered onto the system, case-investigation and treatment details were recorded into the malaria database. A follow-up schedule was generated, and the patient's status was updated when the malaria staff conducted their routine home visits, using mobile phones loaded with the follow-up application module. The module also generated text and graph messages for a summary of malaria cases and basic statistics, and automatically fed to predetermined malaria personnel for situation analysis. Following standard public-health practices, access to the patient database was strictly limited to authorized personnel in charge of patient case management. Results The DTMM module was developed and implemented at the trial site in late November 2008, and was fully functioning in 2009. The system captured 534 malaria patients in 2009. Compared to paper-based data in 2004-2008, the mobile-phone-based case follow-up rates by malaria staff improved significantly. The follow-up rates for both Thai and migrant patients were about 94-99% on Day 7 (Plasmodium falciparum) and Day 14 (Plasmodium vivax) and maintained at 84-93% on Day 90. Adherence to anti-malarial drug therapy, based on self-reporting, showed high completion rate for P. falciparum-infected cases, but lower rate for P. vivax cases. Patients' symptoms were captured onto the mobile phone during each follow-up visit, either during the home visit or at Malaria Clinic; most patients had headache, muscle pain, and fatigue, and some had fever within the first follow-up day (day7/14) after the first anti-malarial drug dose. Conclusions The module was successfully integrated and functioned as part of the malaria prevention and control programme. Despite the bias inherent in sensitizing malaria workers to perform active case follow-up using the mobile device, the study proved for its feasibility and the extent to which community healthcare personnel in the low resource settings could potentially utilize it efficiently to perform routine duties, even in remote areas. The DTMM has been modified and is currently functioning in seven provinces in a project supported by the WHO and the Bill & Melinda Gates Foundation, to contain multi-drug resistant malaria on the Thai-Cambodian border.