Spinal pain (SP) is widely extended among adolescents. The origin of SP can be multifactorial; thus, the present study aimed to estimate the prevalence and risk of SP in high school students and to determine the differences in sagittal spinal curvatures and pelvic tilt, hamstring extensibility, age, anthropometric variables and healthy lifestyle habits dependent on SP between sexes. Two hundred seventy-three teenagers took part in this cross-sectional study. Age, sagittal spinal curvatures, hamstring extensibility, physical activity, sedentary lifestyle, anthropometric variables and health related quality of life (HRQL) were recorded. SP was reported by 16.12% of adolescents. Differences were observed in the HRQL according to SP (p < 0.05). Participants without SP were less sedentary (22.12%) and younger (13.10 years old) than participants with SP (40.91% and 13.66, respectively) (p < 0.05). A logistic regression model showed that both variables were significantly collinear (VIF = 1.01; Durbin-Watson = 2.10). Subjects with low back pain (LBP) had a higher weight, body max index, and hip girth than subjects without pain (p < 0.05). A misalignment in the lumbar spine was associated with LBP for males (Cramer’s V = 0.204, p = 0.022). In conclusion, adolescents with SP were older and had a lower HRQL in all dimensions. SP could be predicted according to age and sedentary habits.