U.S. guidelines for detecting autism emphasize screening and also incorporate clinical judgment. However, most research focuses on the former. Among 1,654 children participating in a multi-stage screening protocol for autism, we used mixed methods to evaluate: (1) the effectiveness of a clinical decision rule that encouraged further assessment based not only on positive screening results, but also on parent or provider concern, and (2) the influence of shared decision-making on screening administration. Referrals based on concern alone were cost-effective in the current study, and reported concerns were stronger predictors than positive screens of time-to-complete referrals. Qualitative analyses suggest a dynamic relationship between parents’ concerns, providers’ concerns, and screening results that is central to facilitating shared decision-making and influencing diagnostic assessment.