This chapter will compare and contrast the properties and applications of two leading antisense molecules, Peptide Nucleic Acids (PNAs)1,2 and Morpholinos3,4. Where appropriate, I discuss the compelling advantages which these two advanced ‘blocker’ types provide relative to ‘modifier’ types of antisense molecules. Some of the properties which are compared include chemical synthesis strategies, chemical stabilities, backbone flexibilities, aqueous solubilities, target selection criteria, target binding affinities, and sequence specificities. Since the mid-1980s, phosphorothioate-linked DNA oligos (S-DNAs) have dominated the antisense field. For many antisense applications, however, advanced non-ionic oligos provide a far better combination of properties, including stability in biological systems, high efficacy and specificity, lack of toxicity, and freedom from non-antisense effects. Prior to the discovery of PNAs by Nielsen et al., I was the first person to conceptualize and to synthesize morpholinos, recognizing their advantages for antisense chemistry. Morpholinos and PNAs share a number of key properties, such as non-ionic backbones whose structures differ radically from that of nucleic acids, resistance to enzymatic degradation, and high (Morpholinos) or very high (PNAs) affinity for complementary RNA sequences. In the context of diagnostics, a particularly valuable property of both structural types is that they strongly pair to complementary genetic sequences under conditions which disrupt secondary structures of nucleic acids. Another particular advantage of morpholinos, and part of the original impetus to develop them, is the fact that they are relatively cheap to produce; the subunits of Morpholinos can be assembled into antisense oligos via simple and efficient coupling to the morpholine nitrogen, without the expensive catalysts and post-coupling oxidation steps required in the production of most nucleic acid analogs. In spite of their many similarities, Morpholinos and PNAs also exhibit significant differences which translate to differing advantages in particular applications. Two key differences which bear on their preferred applications are: 1) PNAs have higher affinities for RNA than do Morpholinos, though both structural types form duplexes with RNA which are more stable than DNA/RNA duplexes, and much more stable than S-DNA/RNA duplexes; 2) Morpholinos are highly soluble in aqueous solutions, generally 5 to 30 mM for 25-mers, depending on sequence, whereas PNAs are typically several hundred-fold less soluble. As a consequence of these differing properties, it appears that PNAs are better suited for high-affinity applications such as targeting short sequences (e.g., the exposed segment of telomerase RNA) and for discriminating between single base differences, as in SNPs (single nucleotide polymorphisms). Conversely, Morpholinos excel in applications which require high aqueous solubility and exquisite discrimination between a targeted mRNA and tens of thousands of non-target mRNAs, such as in vivo applications with developing embryos and other complex systems.