BACKGROUND: The impact of peer relationships has been extensively reported during adolescence, when peer influence is generally considered to be at its greatest. Research on social isolation during childhood has found associations with school achievement, future relationships and adult mental health. Much of the evidence is derived from either parent or child-rated assessment of peer relationships, each of which have their limitations. METHODS: We report findings from Goodman’s Strengths and Difficulties Questionnaire (SDQ), completed by staff in preschool establishments for over 10,000 children in their preschool year (aged 4-5), linked with routine demographic data. Correlations between scores and demographics were explored. Regression models examined the independent relationships between three social isolation variables, taken from the SDQ Peer Relationship Problems, Pro-social Behaviour and Emotional Symptoms subscales, controlling for demographics. RESULTS: There were substantial overlaps between problem scores. Regression models found all social isolation variables to be significantly correlated with social and emotional functioning. Different types of social isolation appeared to relate to different psychological domains, with unpopularity having a stronger relationship with poor pro-social skills, whereas being solitary was more strongly linked to poorer emotional functioning. CONCLUSIONS: Social isolation does have a significant association with reported child social and emotional difficulties, independent of demographic characteristics. The analysis highlights the complexity of measuring social isolation in young children. Different types of social isolation were found to have relationships with specific areas of social and emotional functioning.