Fused Deposition Modeling (FDM) is a 3D printing technique in which a thermoplastic filament is unwound from a coil and extruded through a heated nozzle to produce a part in a layerwise manner. In case of a poor quality of the joint layers, mechanical consistency of the final product will be also poor in consequence. Thermography of parts while they are being printed allows the detection of surface temperature and calculation of temperature gradients within the part, which can lead to thermal stresses and geometric distortions. In our study we investigate (i) the temperature conditions along the extruder, (ii) the melt temperature of the extruded material at the nozzle exit and (iii) the temperature change of the fabricated part during printing on a heated print bed. A mid-wavelength infrared (MWIR) camera was used at a distance of about half a meter from the printed object. The emissivity of the investigated parts was high enough to capture reliable data and reflected radiation from the printhead could be deducted. Calibration of the camera was performed using a black body in thermal equilibrium combined with interpolation following Planck's law for the defined temperature range. During temperature measurement of the extruded material at the nozzle exit, microscope optics was used in order to adjust the spatial frequency of the sensor. We investigated the performance of four different thermoplastic filaments (PLA, ABS, mineral-filled PA, and graphite-filled PLA) during printing of 50x50x5 mm³ objects with 20% infill (45° grid). Heat conduction to the printbed and temporal cooling of the part were analyzed in order to evaluate the potential of thermography for inline monitoring of the 3D printing process. Due to the low conductivity of the thermoplastic polymers heat conduction from the heated printbed to the part was low and rapid cooling by convection was observed, which indicates the importance of temperature control inside the printer to reduce thermal stresses.