Atom trap trace analysis, a novel method based upon laser trapping and cooling, is used to count individual atoms of 41Ca present in biomedical samples with isotopic abundance levels between 10(-8) and 10(-10). The method is calibrated against resonance ionization mass spectrometry, demonstrating good agreement between the two methods. The present system has a counting efficiency of 2x10(-7). Within 1 h of observation time, its 3-sigma detection limit on the isotopic abundance of 41Ca reaches 4.5x10(-10).