3D printing has been adopted into routine use for certain medical applications. Yet, more widespread usage has been hindered by, among other things, unclear legislation. Using legal doctrinal study and legal informatics, we analyzed relevant EU legislation and case law relating to four issues relevant to medical 3D printing (excluding bioprinting or pharma-coprinting): pre-market approval, post-market liability, intellectual property rights, and data protection. Several gaps and uncertainties in the current legislation and interpretations were identified. In particular, we regard the current EU regulatory framework to be quite limiting and inflexible, exemplifying a cautionary approach common in EU law. Recognizing the need to establish high safety standards in order to protect patients, we identify both legal uncertainties and overly restrictive legislation as key factors harmful to innovation. Hence, more adaptive legislation is called for to ensure continuous innovation efforts and enhanced patient outcomes.