We describe analytic approaches for study designs that, like large simple trials, can be better characterized as longitudinal studies with baseline randomization than as either a pure randomized experiment or a purely observational study. We (i) discuss the intention-to-treat effect as an effect measure for randomized studies, (ii) provide a formal definition of causal effect for longitudinal studies, (iii) describe several methods -- based on inverse probability weighting and g-estimation -- to estimate such effect, (iv) present an application of these methods to a naturalistic trial of antipsychotics on symptom severity of schizophrenia, and (v) discuss the relative advantages and disadvantages of each method.