Mental retardation (MR) is a heterogeneous manifestation of central nervous system dysfunction. Chromosomal rearrangements involving subtelomeric regions are believed to be responsible for 5-10 % of all mental retardation cases. Due to relative complexity and high cost of the screening methods used, most studies tested only a selected part of mentally retarded patients. Recently, multiplex ligation dependent probe amplification (MLPA) was adapted for use in subtelomeric screening. This method detects copy number changes of up to 45 nucleic acid sequences in one simple, PCR based reaction. Briefly, by hybridization of probes to the target sequences, followed by a ligation reaction, a copy is made of each target sequence present in the sample. All probe ligation products are subsequently amplified in a multiplex PCR reaction using unique primers attached to the probes. Amplification products are identified and quantified by capillary electrophoresis and copy numbers of target sequences are determined by comparison to a control sample. We used MLPA with SALSA P036b and P070 human telomere test kits to test 4 patients with known subtelomeric rearrangements as positive controls and 35 patients with idiopathic mental retardation and dysmorphic features from Department of Medical Genetics, University Hospital Brno. From these 39 patients, 15 were tested using both kits and in 2 patients subtelomeric aberrations were detected: a terminal Xp/Yp duplication, and a terminal 8p duplication in the patient with primary known terminal 4p deletion. In the rest of 24 patients, tested only by P036B kit, another 3 possible subtelomeric changes were detected. However, these changes must be verified using the second kit or by FISH analysis. We also showed that MLPA is able to detect only subtelomeric aberrations present in minimally 50% of the cells. Our study confirms the diagnostic value of subtelomeric screening, especially in mentally retarded patients with dysmorphic features. This study also demonstrates that MLPA is a fast and reliable screening method for subtelomeric abnormalities, potentially suitable for use in routine diagnostics.