The aim of the study was to estimate the diurnal variations of salivary cortisol in children with autism and healthy children and it's implication on behavior during non-invasive dental procedures. METHODS 50 children with autism and 50 healthy children in the age group between 6 to 12 years of both genders with the need for dental treatment were included in the study. Whole unstimulated saliva was collected from them during early hours of the day and during evenings for 2 consecutive days . The collected saliva was then subjected to electrochemiluminescence assay . Minimum invasive dental procedures like hand scaling, pit and fissure sealants and glass ionomer cement restorations were performed for the participants each time after the saliva sample collection and their behavior during the procedures was rated using Frankl's Behavior Rating Scale. RESULTS Significant correlation was seen between cortisol levels and behavior in children with autism. As cortisol levels increased in children with autism, behavior worsened and as the cortisol levels decreased they showed positive behaviour. CONCLUSIONS Cortisol acts as a stress marker and studying the diurnal variations of salivary cortisol can help us in attaining better knowledge about the behavior pattern and thereby assist us in modifying the behavior modification procedures and treatment planning in this group of special children.