- Background Recent advances in chemotherapeutic treatment of childhood acute leukemia have improved remission rates to about 80%. With the development of novel drugs and treatment protocols adapted for specific individual patients, a simple diagnostic tool for following patients' responses on a daily basis is required. In the present clinical study, we have investigated the usefulness of Fourier transform infrared microscopy (FTIR-MSP) for pre-screening and follow-up of leukemia patients undergoing chemotherapy. Methods Blood samples were collected from leukemia patients before and during treatment as well as from patients with high fever and healthy subjects which served as control groups. Peripheral blood mononuclear cells (PBMCs) were isolated and their spectra obtained using FTIR-MSP. The presence of blasts in bone marrow and other diagnostic and prognostic clinical parameters were determined during follow-up up to 1000 days. Results Leukemia was efficiently indicated by a reduced lipids and elevated DNA absorption of PBMC together with additional characteristic spectral bands. These diagnostic markers were used for monitoring the biochemical changes in PBMCs during chemotherapy. The trends of several markers were found to be in agreement with blast percentage as determined by flow cytometry. Conclusions Our findings reveal the utility of FTIR-MSP for leukemia pre-screening independently of symptoms common to leukemia. Furthermore, FTIR-MSP supplies precursor indication regarding patient response to treatment compared to current methods. General significance This preliminary study shows a great potential of FTIR-MSP as a complementary tool for childhood leukemia pre-screening and follow-up which may allow faster response to critical problems arise during treatment.