Background Stunting is prevalent by the age of 6 mo in the indigenous population of the Western Highlands of Guatemala. Aim The objective of this study was to determine the time course and predictors of linear growth failure and weight-for-age in early infancy. Study Design and Subjects One hundred and forty eight term newborns had measurements of length and weight in their homes, repeated at 3 and 6 mo. Maternal measurements were also obtained. Results Mean ± SD length-for-age Z-score (LAZ) declined from newborn -1.0 (1.01) to -2.20 (1.05) and -2.26 (1.01) at 3 and 6 mo respectively. Stunting rates for newborn, 3 and 6 mo were 47%, 53% and 56% respectively. A multiple regression model (R2 = 0.64) demonstrated that the major predictor of LAZ at 3 mo was newborn LAZ with the other predictors being newborn weight-for-age Z-score (WAZ), gender and maternal education*maternal age interaction. Because WAZ remained essentially constant and LAZ declined during the same period, weight-for-length Z-score (WLZ) increased from -0.44 to +1.28 from birth to 3 mo. The more severe the linear growth failure, the greater WAZ was in proportion to the LAZ. Conclusion The primary conclusion is that impaired fetal linear growth is the major predictor of early infant linear growth failure indicating that prevention needs to start with maternal interventions.