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Mother-infant interactions were investigated to: (a) determine the feasibility of simultaneously conducting functional analyses on two individuals' behaviors in an unstructured setting; (b) compare functional analysis results across the Motivational Assessment Scale (MAS), Functional Assessment Interview Form (FAIF), and videotaped observational data analyzed using conditional probabilities (CP); and (c) compare parenting stress and social support, and infant developmental level with patterns of interaction. Twenty-one mother-infant dyads, nine with developmental delays (DD), having infants between 12 and 36 months of age participated. Five home visits were conducted. In the first, mothers completed a questionnaire and interview regarding their infants' challenging behavior. In the next four visits, dyads were instructed to behave naturally and were videotaped for 10 minutes interacting in each of four situations (Alone, Difficult, Eat, Play). Videotaped interactions were coded using 13 pre-determined behavioral codes in a real-time data entry computer program. CP analyses and graphs were used to determine functions of both mother and infant behavior. Determining the functions of behavior in this manner was inefficient. However, determinations of function of infant behavior were in agreement with functions determined through unplanned direct observations in all cases, and were in agreement with the FAIF and MAS in 85% of cases. No one package-type intervention based upon presumed functions of challenging behavior would be effective for the population with DD, but may be for the typically-developing population. Clinicians are recommended to use direct observation in combination with the FAIF rather than CP analyses in determining functions of behavior and designing interventions for dyads with an infant with DD. Further research should investigate the effect of determining function of mother behavior on intervention efficacy and devise more efficient, and potentially more accurate, methods to determine function of mother behavior.