Humans are endowed with an innate ability to produce rhythmic expressions that reveal intentions and feelings and attune their rhythmic behavior with that of another person who is attentive and affectionate. A small number of studies in children with Autism Spectrum Disorder (ASD) show that the rhythmic patterns of their expressions differ from those observed in typically developing (TD) children, and they are not well attuned to the expressions of their communicative partner. The aim of the present study was to assess rhythmic patterns in mother-child cooperative communication in children with ASD compared to TD children. Ten children with ASD and ten TD children, matched for mental age, were videotaped in their homes during play sessions with their mothers. For the microanalysis, the Eudico Linguistic Annotator was used and a coding system was developed for the annotation of communicative modalities. Results showed that children with ASD are less likely to initiate joint action and respond to mother's efforts for mutual interaction. Exploratory/relational play was their preferred means for initiation. Maternal responses were provided mainly through the modality of gaze for both ASD and TD children. Moreover, the gaze direction of the dyad indicates that ASD partners focus mainly on different directions, whereas TD partners look mostly at the same object. Analysis of their affective states demonstrates that affect attunement is difficult to achieve. These findings indicate that children with ASD exhibit disturbances in rhythmic interaction with their caregiver, which reveal severe deficiencies in the motive for interpersonal awareness.