Background The surge of methamphetamine use has been a complicating factor compounding the U.S. poly-drug use landscape. Infections of blood-borne virus including hepatitis B virus (HBV), hepatitis C virus (HCV) and HIV, arising from methamphetamine use continue to grow. This study aimed to examine the risk factors associated with blood-borne infections from HBV, HCV and HIV among people who used methamphetamine. Methods Methamphetamine users were identified from five National Health and Nutrition Examination Survey (NHANES) cohorts from 2007 to 2016. We examined the association of sexual activities (sexual partners, sexual identity), drug use behaviors (poly-drug use, injection drug use, number of times drug use, age started using methamphetamine), demographics and socio-economic status with blood-borne infections using bivariate and multivariable logistic regressions. Results There were 1,075 participants representing approximately 11,319,270 methamphetamine users in the U.S. with prevalence of blood-borne infections 13.4 per 100,000. Multivariable logistic regression analyses showed significant associations of blood-borne infections with age 50-59 years (adjusted odds ratio 6.32, 95% CI 1.35-29.69), living within poverty index 1-1.9 (2.80; 1.33 – 5.88), living below the poverty threshold (2.46; 1.14 – 5.28), having lower than high school education (3.57; 1.74 – 7.33), identified as men who have sex with men (MSM) (54.24; 13.80 – 213.24), using methamphetamine with other substances (5.86; 1.50 – 22.87), injection drug use (3.77; 1.93 – 7.36), and started using methamphetamine at age above 25 (2.18; 1.05 – 4.54). Conclusions Polysubstance use, injection drug use, and MSM were strongly associated with increased risk of blood-borne infections among methamphetamine users.