We present 5 to 36 \micron mid-infrared spectra of 82 young stars in the \sim 2 Myr old Chamaeleon I star-forming region , obtained with the Spitzer Infrared Spectrograph ( IRS ) . We have classified these objects into various evolutionary classes based on their spectral energy distributions and the spectral features seen in the IRS spectra . We have analyzed the mid-IR spectra of Class II objects in Chamaeleon I in detail , in order to study the vertical and radial structure of the protoplanetary disks surrounding these stars . We find evidence for substantial dust settling in most protoplanetary disks in Chamaeleon I . We have identified several disks with altered radial structures in Chamaeleon I , among them transitional disk candidates which have holes or gaps in their disks . Analysis of the silicate emission features in the IRS spectra of Class II objects in Cha I shows that the dust grains in these disks have undergone significant processing ( grain growth and crystallization ) . However , disks with radial holes/gaps appear to have relatively unprocessed grains . We further find the crystalline dust content in the inner ( \lesssim 1-2 AU ) and the intermediate ( \lesssim 10 AU ) regions of the protoplanetary disks to be tightly correlated . We also investigate the effects of accretion and stellar multiplicity on the disk structure and dust properties . Finally , we compare the observed properties of protoplanetary disks in Cha I with those in slightly younger Taurus and Ophiuchus regions and discuss the effects of disk evolution in the first 1-2 Myr .