Homocysteine is an amino acid which plays several important roles in human physiology and is an important biomarker for possible deficiencies of various vitamins (vitamin B₆ and B₁₂, folic acid). In this work GC-MS method was used to determine the levels of homocysteine in the urine of autistic and healthy children. The levels of homocysteine in urine samples from 34 autistic and 21 healthy children were 2.36 ± 1.24 and 0.76 ± 0.31 (mmol∙mol⁻¹ creatinine), respectively. The higher level of homocysteine in autistic children may indicate deficiencies of folic acid and vitamins B₆ and B₁₂ in nutrition of these children. The results of this work were taken into consideration in the nutrition of autistic children treated in the Navicula Centre of Diagnosis and Therapy of Autism in Łódź (Poland).