Congenital cystic adenomatoid malformations (CCAMs) are benign masses of non-functional lung tissue developing from an overgrowth of the terminal bronchioles with subsequent suppressing of alveolar growth. For the first time CCAMs are studied by Raman mapping and Fourier transform infrared (FTIR) imaging. Both vibrational spectroscopic methods are able to analyze the biochemical composition of tissues and their pathological changes at the molecular level. Cryosections were prepared on calcium fluoride substrates from CCAMs and from normal lung tissue of two infant patients who underwent surgery. Raman maps were collected at a step size of 100 µm in order to assess the whole tissue section and at a smaller step size of 10 µm in order to resolve details in selected areas. FTIR images were collected in the macroscopic and microscopic modes. Data sets were segmented by cluster analysis and the mean spectra of each cluster were compared. At low lateral resolution a lower red blood cell content and higher lipid content were found in CCAMs than in normal lung tissue. At higher lateral resolution, accumulations of lipids and glycogen were identified in CCAMs. The lipid aggregates contain a high concentration of phosphatidylcholine. It is discussed how the combined application of Raman mapping and FTIR imaging might improve the differential diagnosis of lung malformations and how both modalities might be applied to other bioanalytical and biomedical problems in the future.