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In recent years, targeted minimum loss-based estimation methodology has been used to develop estimators of parameters in longitudinal data structures (Gruber and van der Laan 2012; Petersen, Schwab, Gruber, Blaser, Schomaker, and van der Laan 2014; Schnitzer, Moodie, van der Laan, Platt, and Klein 2013). These methods are implemented in the ltmle package for R. The ltmle package provides methods to estimate intervention-specific means and measures of association including the average treatment effect, causal odds ratio and causal risk ratio and parameters of a longitudinal working marginal structural model. The package allows for multiple time point treatments, time-varying covariates and right censoring of the outcome. In this paper we described the usage of the ltmle package and provide examples.