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Introduction The need for cost effective surveillance of emerging human and veterinary pathogens has triggered a resurgence in research on environmental sampling methods, a process in which filter paper could play a role. The objective of this research was to compare the recovery of nucleic acids from paper products under laboratory conditions. Methods In Experiment 1, commercially available paper products (n = 9) were saturated with water (1000 to 3000 µl) and the volume of decanted liquid measured and analyzed (linear regression). In Experiment 2, 4 paper products from Experiment 1 were evaluated for the release of RT-qPCR-detectable porcine reproductive and respiratory syndrome virus (PRRSV) RNA and porcine epidemic diarrhea virus (PEDV) RNA. Specifically, products were inoculated with PRRSV and PEDV, dried, subjected to 9 elution conditions (3 elution buffers × 3 soaking times), and tested by RT-qPCR. Thereafter, results were normalized and re-expressed as efficiency-standardized Cqs (ECqs). Results and Discussion In Experiment 1, significant differences in recovery were observed across products and volumes (p < 0.05), with paper products 3 and 4 releasing the highest volumes. In Experiment 2, linear regression analysis showed that paper type, elution buffer, virus dilution, and their interactions affected viral RNA recovery (p < 0.05). AUC analysis showed no significant difference in PRRSV RNA detection between buffer-specific positive controls and product 3 eluted with lysis buffer or water. Similarly, no difference was detected in PEDV RNA detection between the positive control eluted with lysis buffer and products 3 and 4 eluted with lysis buffer. These results demonstrated that the choice of filter paper and the procedures used for viral RNA detection significantly affect target recovery.