Heat butter, brown sugar, corn syrup, and sweetened condensed milk in a heavy saucepan over Medium-High heat.
Bring to a boil, stirring occasionally. Continue cooking and stirring until a candy thermometer reaches 248 degrees, about 30 minutes.
Remove from heat, and stir in vanilla.
Dip each pretzel rod into caramel, turning to completely coat.
Allow excess to drip off, then place on parchment paper to set.*
Place bittersweet chocolate chips in a large bowl and heat in the microwave for 1 minute on HIGH. Stir, then continue cooking and stirring in 15 second intervals until chocolate is melted and smooth.
Dip caramel covered pretzels in the melted chocolate, using a large spoon to cover all sides.***
Place on parchment paper to set.
Place milk chocolate chips in a large bowl and heat in the microwave for 1 minute on HIGH. Stir, then continue cooking and stirring in 15 second intervals until chocolate is melted and smooth.
Hold chocolate covered pretzels over the bowl of melted milk chocolate. Use a large spoon to drizzle the chocolate randomly over the pretzels.
Set on parchment paper to set.
If caramel runs off the pretzels too much, squish it back into shape with your fingers.
Be very careful when lifting caramel covered pretzels off the parchment paper!! They will snap in half if you apply too much pressure. Hold the pretzel, lift and pull the parchment paper from below to remove.
Using tempered chocolate will keep them from developing spots over time. Or you could always temper your chocolate if you know how.