Background This survey was designed to study the gender difference in physical growth of 1113 Pakistani children (646 male and 467 female) living in Bahrain and to compare growth with their Bahraini and Pakistani counterparts. Methods Measurements of height, weight, mid-arm circumference, biceps, triceps, subscapular and suprailiac skinfold thickness were carried out using the standard methods, and the median values for height and weight were plotted against the National Center for Health Statistics (NCHS) standard charts. Results The median weight of the boys was below the 25th percentile rising slightly above the 25th percentile at 12 years. The median height was also below the 25th percentile touching the 25th percentile only between 10-12 and 17 years. In girls, the median weight touched the 50th percentile at 15 years, followed by a fall to the 5th percentile between 16 and 17 years of age while the median height touched the 5th percentile at 17 years of age. The median body mass index (BMI) values were above the 50th percentile between 13 and 15 years in boys, and below the 50th percentile at all ages in girls. The median triceps skinfold thickness in boys was above the 50th percentile between 10-15 and 17 years in boys and in girls it was mostly below the 50th percentile rising above 50th percentile at 14, 15 and 17 years of age. Conclusion The height and weight of the study group was similar to that of children residing in Pakistan for both the genders, but lower than their Bahraini counterparts for most age groups compared. Furthermore, Pakistani boys residing in Bahrain were taller after 14 years of age and heavier after 16 years of age compared to their female counterparts.