Drug delivery is a hurdle that has to be overcome every time a new therapeutic approach is devised or tested in a new tissue. Identifying peptides for conjugation to the therapeutic compound to improve delivery to the target tissue or cells could help improve therapy efficacy. We make use of phage display biopanning in two mouse models for Duchenne muscular dystrophy (DMD) to find muscle homing peptides to advance therapeutic uptake of antisense oligonucleotides (AON). AONs are pieces of short, modified RNA that can restore the distorted reading frame of dystrophin that is causing DMD. Uptake of these AONs into muscle tissues is currently suboptimal. Following in vivo phage display biopanning, we made use of next-generation sequencing to ensure that our analysis could be carried out as unbiased as possible. A selection strategy was devised to screen for muscle homing peptides, resulting in a list of potential muscle homing peptides that can be tested further to check for improved delivery. In this chapter, we describe the protocols that were carried out and point out notable steps to consider when executing this method.