| Number | In Season | Title | Original Air Date | Production code |
|---|---|---|---|---|
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Rainforest Shmainforest | |||
| The boys travel to the Costa Rica as a part of the "Getting Gay with Kids" choir tour. | Apr 7, 1999 | 32 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Spontaneous Combustion | |||
| When the citizens of South Park start exploding randomly, The mayor enlists Stan's dad, the resident geologist, to find a solution to the problem. | Apr 14, 1999 | 33 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | The Succubus | |||
| Chef's parents arrive in South Park from Scotland fresh from an encounter with the Loch Ness Monster to attend Chef's wedding. | Apr 21, 1999 | 34 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Tweek Vs. Craig | |||
| The boys instigate a fight between Tweek and Craig in shop class. Meanwhile, Mr. Adler, the shop teacher, is haunted by a recurring dream of his lost love. | Jun 23, 1999 | 35 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Jakovasaurs | |||
| The boys discover a prehistoric creature called a Jackovasaur while camping at Stark's Pond. | Jun 16, 1999 | 36 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Sexual Harassment Panda | |||
| After Sexual Harassment Panda "educates" the children, Cartman sues Stan for sexual harassment, and a flurry of other lawsuits follow. | Jul 7, 1999 | 37 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Cat Orgy | |||
| While all the adults are gathering at Mr. Mackey's house to watch a meteor shower Shelly Marsh is left babysit Cartman. | Jul 14, 1999 | 38 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Two Guys Naked in a Hot Tub | |||
| Stan's parents drag him along to Mr. Mackey's meteor shower party, where he is sent down into the basement to play with Pip, Butters and Dougie. | Jul 21, 1999 | 39 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Jewbilee | |||
| Kyle invites Kenny to join him and Ike at Jewbilee, a camp for Jewish kids. | Jul 28, 1999 | 40 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Chinpoko Mon | |||
| Stan,Kyle,Cartman and Kenny are caught up in the latest fad from Japan: Chinpoko Mon! | Nov 3, 1999 | 41 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Starvin' Marvin in Space | |||
| Starvin' Marvin returns to South Park with an alien spaceship and enlists Cartman, Stan, Kyle and Kenny's help to seek out a new home for his starving people. | Nov 17, 1999 | 42 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Korn's Groovy Pirate Ghost Mystery | |||
| Korn comes to South Park for a Halloween concert and helps the boys solve a spooky pirate ghost mystery. | Oct 27, 1999 | 43 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Hooked on Monkey Fonics | |||
| To help Cartman win the school spelling bee, Cartman's Mom gives him the Hooked on Monkey Fonics spelling system. | Nov 10, 1999 | 44 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | The Red Badge of Gayness | |||
| Cartman has visions of glory as he suits up for the Confederacy in the annual reenactment of a Civil War battle, and leads the drunken rebels to defeat the union. | Nov 24, 1999 | 45 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Mr. Hankey's Christmas Classics | |||
| An extravaganza of holiday songs are performed in unique South Park style, hosted by Mr. Hankey. | Dec 1, 1999 | 46 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | Are You There, God? It's Me, Jesus | |||
| People from all over the world start to gather outside Jesus' house waiting for a millennium miracle. | Dec 29, 1999 | 47 | ||
| http://southparkstudios.mtvnimages.com/images/south_park/episode_thumbnails/s{{{S}}}e{{{E}}}_480.jpg | World Wide Recorder Concert | |||
| The children of South Park are invited to Arkansas for the "Four Million Child Blow 2000," the first worldwide recorder concert. | Jan 12, 2000 | 48 | ||
