Early childhood is an important nutritional period that involves the transition from a milk-based diet to ordinary foods. A systematic review was conducted of studies that applied whole-of-diet analysis of children aged 1−5 years to examine associations between diet and nutrition, health, and development. Literature searches identified 40 articles using dietary indices, principal component analysis, or cluster analysis. Reports that applied indices (n = 23, 18 indices) were cross-sectional, and most measured diet quality or variety. Articles reporting principal component or cluster analyses (n = 17) described between two and six dietary patterns, and most identified healthy, unhealthy, and traditional patterns. In cross-sectional analyses, mixed associations were found between index or pattern scores and nutrient intake (n = 10), nutritional biomarkers (n = 1), and anthropometry (n = 10). Five reports from two birth cohorts showed healthier dietary patterns were associated with better lean mass, cognition, and behavior, but not with bone mass or body mass index at later ages. Few studies have characterized the diets of children under 5 years of age and linked diet with health. Given the limited evidence, research establishing the predictive validity of whole-of-diet methods in childhood is needed.