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We don't know. Most studies are related to drug use and fertility, not genetic alterations passing on to offspring. Few people use only one drug for meaningful drug studies along those lines let alone separating the affects of multiple drugs (e.g. alcohol and cocaine) from the affects other physical deviations.
While some associations have been made, like men's methamphetamine use and heart abnormalities in offspring, cause and affect has not been established for most drugs. We can't say they cause problems; but, we can't rule it out either. That there aren't enough studies to rule it out by even just a preponderance of the evidence has been one of the obstacles in getting drugs like marijuana legalized.
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