Background: Father absence and its consequent impacts on family socioeconomic status (SES), children’s growth are important issues in human bio-social research. Objectives: The present study aimed at understanding differential height growth, rate of stunting, age at menarche (AAM, early or not early) of school-going girls and their family SES in cases of presence and absence of fathers in families. Methods: A mixed-longitudinal study was done during 2009-10 and 2010-11 among 9 to 17 year-old 540 girls in Merida, Yucatan. Participants of the study were 9-15 year-old 87 girls whose menarche occurred in between first and second rounds of the survey. Based on civil condition of the parents, girls had either both parents (63 cases) or only mother (24 cases) in the family. Retrospective information of AAM and prevalence of stunting (short height for age) were recorded. Early menarche (EM) was < 12 years of age. SES indicators included: crowding index (CI= number of family members/number of bedrooms in a house), mother’s education (secondary or above) and occupation (housewife or working), daughter’s school type (public or private). Results: Higher proportions of crowded families (CI>= 3.0), working mothers with secondary education, daughters studying in public schools, stunting, and not EM were associated with father absence. Conclusion: Situation of girls and mothers were worse in absence of father.